ScienceWeek

SCIENCEWEEK

February 2, 2007

Vol. 11 - Number 5

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I have never met a bored biologist... Biologists suffer from paranoia, frustrated ambition, angst about their sex lives, lack of hard cash, and all the usual frets that beset mankind. But they are not bored.

-- Martin Wells

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Contents (full text below):

1. Developmental Biology: Stem Cells and Asymmetric Mitosis

2. Chemistry: On Single-Molecule Catalysis

3. Theoretical Biology: Biology's Next Revolution

4. Atomic Physics: On The Social Life of Atoms

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New Books Noted:

Conversations on Consciousness. What the Best Minds Think About the Brain, Free Will, and What It Means to Be Human. Susan Blackmore. Oxford University Press, New York, 2007. Paperback: 282 pp., illus. ISBN 9780195179590. More information at: http://www.amazon.com/exec/obidos/ASIN/0195179595/scienceweek

The Future of Everything. The Science of Prediction. David Orrell. Thunder's Mouth (Avalon Publishing Group), New York, 2007. Hardback: 457 pp., illus. ISBN 9781560259756. More information at: http://www.amazon.com/exec/obidos/ASIN/1560259752/scienceweek

How the Earthquake Bird Got Its Name and Other Tales of an Unbalanced Nature. H. H. Shugart. Yale University Press, New Haven, CT, 2007. Paperback: 239 pp., illus. ISBN 9780300122701. More information at: http://www.amazon.com/exec/obidos/ASIN/0300122705/scienceweek

The Human Touch. Our Part in the Creation of a Universe. Michael Frayn. Metropolitan (Henry Holt), New York, 2007. Hardback: 512 pp. ISBN 9780805081480. More information at: http://www.amazon.com/exec/obidos/ASIN/0805081488/scienceweek

An Imaginary Tale. The Story of [the square root of minus one]. Paul J. Nahin. Princeton University Press, Princeton, NJ, 2007. Paperback: 293 pp., illus. ISBN 9780691127989. More information at: http://www.amazon.com/exec/obidos/ASIN/0691127980/scienceweek

Smithsonian Intimate Guide to Human Origins. Carl Zimmer. Collins (HarperCollins), New York, 2007. Paperback: 176 pp., illus. $15.95. ISBN 9780061196676. More information at: http://www.amazon.com/exec/obidos/ASIN/0061196673/scienceweek

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1. DEVELOPMENTAL BIOLOGY: STEM CELLS AND ASYMMETRIC MITOSIS

The following points are made by A.C. Spradling and Y. Zheng (Science 2007 315:469):

1) The stem cells that sustain metazoan tissues face a difficult challenge. Each time a stem cell divides -- it can divide indefinitely -- it risks damage from errors in the duplication and segregation of genetic and cellular material that could stunt its vitality or propel it toward a cancerous state. Normally, each division must be asymmetric to ensure that only one daughter cell differentiates, while the other becomes a stem cell, thus renewing the stem cell population. Yet stem cells safely grow and divide many more times than other cell types, including their own daughters.

2) New work (1) examines the role of one of the most fundamental cellular components in supporting stem cell function -- the centrosome. Centrosomes organize the microtubule-rich mitotic spindle that directs how chromosomes and other materials are distributed between daughter cells at cell division (mitosis). The authors show that male germline stem cells in the fruit fly Drosophila melanogaster differentially position their mother and daughter centrosomes during mitosis. As part of this strategy, which ensures asymmetric division, the stem cell permanently retains the mother centrosome across many cell divisions, raising the possibility that differential centrosomal inheritance is essential to stem cell biology.

3) Unlike other known animal cell organelles, the two centrosomes inherited by daughter cells at division are not identical. All normal cells initially have one centrosome, comprising a mother and daughter centriole as well as pericentriolar material. The mother centriole contains structures and proteins that are absent from the daughter centriole, and it nucleates more microtubules than the daughter. During each cell division cycle, the centrosome replicates. The mother centrosome retains the original mother centriole. In contrast, the daughter centrosome undergoes maturation during mitosis and during the G1 phase of the next cell division cycle, converting its inherited daughter centriole into a new mother centriole (2). Whether this intrinsic asymmetry facilitates asymmetric stem cell division has remained a mystery.

4) Yamashita et al. (1) took advantage of centrosomal asymmetry to follow the fates of mother and daughter centrosomes during germline stem cell division in the testis of Drosophila. These germline stem cells, which give rise to sperm, have already divided 12 or more times when they become established in their niche, adjacent to stromal cells known as the hub. Germline stem cells complete as many as 30 additional cell cycles over the life of the animal, each time sustaining themselves while producing one non-stem cell daughter, the gonialblast. Each gonialblast divides just six times before differentiating.

5) The authors genetically engineered flies to produce a centrosomal protein, known as PACT, tagged with green fluorescent protein. By inducing the expression of this fluorescent protein at different times, they could selectively label either mother or daughter centrosomes. Mother centrosomes were almost always located near the hub, which ensured that after mitosis they would be inherited by the daughter that remains in the niche and remains a stem cell. Daughter centrosomes, on the other hand, always migrated to the opposite end of the stem cell and were inherited by the daughter cell destined to become a gonialblast. Thus, germline stem cells retain their mother centrosome from the time they first enter their niche.(3-5)

References (abridged):

1. Y. M. Yamashita, A. P. Mahowald, J. R. Perlin, M. T. Fuller, Science 315, 518 (2007).

2. M. Delattre, P. Gonczy, J. Cell Sci. 117, 1619 (2004).

3. Y. M. Yamashita, D. L. Jones, M. T. Fuller, Science 301, 1547 (2003).

4. A. Gromley et al., Cell 123, 75 (2004).

5. G. Emery et al., Cell 122, 763 (2005).

Science http://www.sciencemag.org

ScienceWeek http://scienceweek.com

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2. CHEMISTRY: ON SINGLE-MOLECULE CATALYSIS

The following points are made by Ian Smith (Science 2007 315:470):

1) To some people, the word "catalysis" conjures up images of large-scale industrial processes. For example, the Haber process, discovered about 100 years ago, makes use of supported iron catalysts to speed up the conversion of nitrogen and hydrogen to ammonia at moderate temperatures. Worldwide, this process is responsible for the annual manufacture of more than 100 million metric tons of ammonia (1). In contrast, new work (2) addresses a fundamental question: Can single molecules serve as catalysts? That is, can individual molecules accelerate chemical reactions?

2) This question is best answered by experiments in the gas phase, where the overall reaction comprises a series of elementary reactions, each involving a small number of molecules. One well-known example is the catalytic destruction of ozone in the upper atmosphere by species such as halogen atoms, nitric oxide, and hydroxyl radicals (3). These species (X) participate in chain reactions (X + O3 rarrow XO + O2 and XO + O rarrow X + O2), whose net effect is to speed up the conversion of "odd oxygen" (O atoms and O3 molecules) to dioxygen O2, thereby lowering the amount of ozone present in the stratosphere.

3) This destruction of ozone can be thought of as an example of homogeneous catalysis (the catalyst is in the same phase as the reactants), familiar in reactions in solution. By contrast, Vöhringer-Martinez et al.(2) provide an example of gas-phase catalysis more akin to heterogeneous catalysis. They report that the reaction between hydroxyl radicals and acetaldehyde, OH + CH3CHO rarrow H2O + CH3O, is accelerated by the participation of single molecules of water. They argue convincingly that this is because hydrogen-bonded complexes of CH3CHO and H2O form and that these complexes react faster with OH radicals than do individual molecules of CH3CHO. The binding to water is thus analogous to binding to a surface in heterogeneous catalysis.

4) Their experiments make use of gas mixtures cooled to several different temperatures, as low as 58 K, by expansion through a convergent-divergent "Laval" nozzle (4). Information about the rate of reaction is then obtained by a standard method: OH radicals are generated by pulsed laser photolysis of hydrogen peroxide, and the rate of their reactive loss is measured with the use of a second laser that induces the OH radicals to fluoresce. The decrease in the fluorescence signal as the time delay between the two laser pulses is increased provides information about the reaction rate. Adding water to the expanded gas increases the rate of loss of OH, especially at the lowest temperatures of the experiments.(5)

References (abridged):

1. J. A. Pool, E. Lobkovsky, P. J. Chirik, Nature 427, 527 (2004).

2. E. Vöhringer-Martinez et al., Science 315, 497 (2007).

3. R. P. Wayne, Chemistry of Atmospheres (Oxford Univ. Press, Oxford, ed. 3, 2000), p. 164.

4. I. W. M. Smith, B. R. Rowe, Acc. Chem. Res. 33, 261 (2000).

5. E. E. Greenwald, S. W. North, Y. Georgievskii, S. J. Klippenstein, J. Phys. Chem. A 109, 6031 (2005).

Science http://www.sciencemag.org

ScienceWeek http://scienceweek.com

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3. THEORETICAL BIOLOGY: BIOLOGY'S NEXT REVOLUTION

The following points are made by N. Goldenfeld and C. Woese (Nature 2007 445:369):

1) One of the most fundamental patterns of scientific discovery is the revolution in thought that accompanies a new body of data. Satellite-based astronomy has, during the past decade, overthrown our most cherished ideas of cosmology, especially those relating to the size, dynamics and composition of the Universe. Similarly, the convergence of fresh theoretical ideas in evolution and the coming avalanche of genomic data will profoundly alter our understanding of the biosphere -- and is likely to lead to revision of concepts such as species, organism and evolution. Here we explain why we foresee such a dramatic transformation, and why we believe the molecular reductionism that dominated twentieth-century biology will be superseded by an interdisciplinary approach that embraces collective phenomena.

2) The place to start is horizontal gene transfer (HGT), the non-genealogical transfer of genetic material from one organism to another -- such as from one bacterium to another or from viruses to bacteria. Among microbes, HGT is pervasive and powerful -- for example, in accelerating the spread of antibiotic resistance. Owing to HGT, it is not a good approximation to regard microbes as organisms dominated by individual characteristics. In fact, their communications by genetic or quorum-sensing channels indicate that microbial behaviour must be understood as predominantly cooperative.

3) In the wild, microbes form communities, invade biochemical niches and partake in biogeochemical cycles. The available studies strongly indicate that microbes absorb and discard genes as needed, in response to their environment. Rather than discrete genomes, we see a continuum of genomic possibilities, which casts doubt on the validity of the concept of a "species" when extended into the microbial realm. The uselessness of the species concept is inherent in the recent forays into metagenomics -- the study of genomes recovered from natural samples as opposed to clonal cultures. For example, studies of the spatial distribution of rhodopsin genes in marine microbes suggest such genes are "cosmopolitan", wandering among bacteria (or archaea) as environmental pressures dictate.

4) Equally exciting is the realization that viruses have a fundamental role in the biosphere, in both immediate and long-term evolutionary senses. Recent work suggests that viruses are an important repository and memory of a community's genetic information, contributing to the system's evolutionary dynamics and stability. This is hinted at, for example, by prophage induction, in which viruses latent in cells can become activated by environmental influences. The ensuing destruction of the cell and viral replication is a potent mechanism for the dispersal of host and viral genes.

5) It is becoming clear that microorganisms have a remarkable ability to reconstruct their genomes in the face of dire environmental stresses, and that in some cases their collective interactions with viruses may be crucial to this. In such a situation, how valid is the very concept of an organism in isolation? It seems that there is a continuity of energy flux and informational transfer from the genome up through cells, community, virosphere and environment. We would go so far as to suggest that a defining characteristic of life is the strong dependency on flux from the environment -- be it of energy, chemicals, metabolites or genes.

6) Nowhere are the implications of collective phenomena, mediated by HGT, so pervasive and important as in evolution. A computer scientist might term the cell's translational apparatus (used to convert genetic information to proteins) an 'operating system', by which all innovation is communicated and realized. The fundamental role of translation, represented in particular by the genetic code, is shown by the clearly documented optimization of the code. Its special role in any form of life leads to the striking prediction that early life evolved in a Lamarckian way, with vertical descent marginalized by the more powerful early forms of HGT.(1-4)

References:

1) Frigaard, N., Martinez, A., Mincer, T. & DeLong, E. Nature 439, 847–850 (2006).

2) Sullivan, M. et al. PLoS Biol. 4, e234 (2006).

3) Pedulla, M. et al. Cell 113, 171–182 (2003).

4) Vetsigian, K., Woese, C. & Goldenfeld, N. Proc. Natl Acad. Sci. USA 103, 10696–10701 (2006).

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4. ATOMIC PHYSICS: ON THE SOCIAL LIFE OF ATOMS

The following points are made by Maciej Lewenstein (Nature 2007 445:372):

1) Counting individual quantum-mechanical objects such as the particles of a complex many-body system -- whether photons, electrons, atoms or something else -- is an efficient way to learn about the properties of both the system and of the particles being counted. Fifty years ago, Robert Hanbury Brown and Richard Twiss (1) published the results of the paradigmatic experiment of this sort, in which they counted joint detections, in two separate detectors, of photons from distant stars. The two-photon correlations clearly showed that the photons liked to arrive bunched up in groups. Jeltes et al.(2) use less well-travelled particles for their investigations -- ultracold helium atoms. But they are able, for the first time in the same experiment, to compare and contrast the Hanbury Brown–Twiss (HBT) effect for both "bosonic" and "fermionic" particles.

2) Although the original HBT effect can easily be understood within the framework of classical physics, explaining it in quantum-mechanical terms is more tricky. It requires acknowledging that photons are particles of integer spin, or bosons. These particles are far more gregarious than their fermion (half-integer-spin) cousins, and the bunching phenomenon can be described as the result of constructive interference of the quantum-mechanical probability amplitudes of two (bosonic) photons reaching the detectors. This explanation led Roy Glauber (3) to formulate modern photon-counting theory within the framework of quantum electrodynamics, the quantum field theory of the electromagnetic force. The result was the birth of modern quantum optics, an achievement crowned by a Nobel prize for Glauber in 2005.

3) Atoms of the helium isotope 4He are also bosons, because they consist of a total of six half-integer-spin particles: four nucleons (two protons and two neutrons) and two orbiting electrons. Experiments with ultracold, metastable 4He have not only famously allowed the observation of Bose–Einstein condensation (the phenomenon of many bosons all adopting the same quantum state), but have also opened the way to precise time-resolved and position-sensitive counting experiments in atomic systems. These helium atoms have a very long lifetime if unperturbed, but can be detected with almost perfect efficiency in micro-channel plate and delay-line detectors.

4) The first direct observation of the bunching of 4He atoms --the atomic HBT effect -- came two years ago (4). The same authors are part of the team that has now seen (2) the analogous effect in 3He atoms, whose two electrons and three nucleons (only one neutron this time) make them fermions. Fermions obey the Pauli exclusion principle, so unlike bosons they do not like being in the same place at the same time. What Jeltes et al.(2) observe in the case of 3He, therefore, is not the bunching characteristic of bosons, but "antibunching" resulting from the destructive interference of the fermions' probability amplitudes.(5)

References (abridged):

1. Hanbury Brown, R. & Twiss, R. Q. Nature 177, 27–29 (1956).

2. Jeltes, T. et al. Nature 445, 402–405 (2007).

3. Glauber, R. J. in Quantum Optics and Electronics (eds DeWitt, B., Blandin, C. & Cohen-Tannoudji, C.) 63–185 (Gordon & Breach, New York, 1965).

4. Schellekens, M. et al. Science 310, 648–651 (2005).

5. Hellweg, D. et al. Phys. Rev. Lett. 91, 010406 (2003).

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